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Introduction: Spontaneous control of chronic-phase HIV/SIV viremia is often associated with the expression of specific MHC class I allotypes. HIV/SIV-specific CD8+ cytotoxic T lymphocytes (CTLs) restricted by these MHC class I allotypes appear to be critical for viremic control. Establishment of the elite controller (EC) phenotype is predictable in SIVmac239-infected Indian rhesus macaques (RMs), with approximately 50% of Mamu-B*08 + RMs and 20% of Mamu-B*17 + RMs becoming ECs. Despite extensive characterization of EC-associated CTLs in HIV/SIV-infected individuals, the precise mechanistic basis of elite control remains unknown. Because EC and non-EC viral load trajectories begin diverging by day 14 post-infection, we hypothesized that hyperacute innate immune responses may contribute to viremic control. Methods: To gain insight into the immunological factors involved in the determination of EC status, we vaccinated 16 Mamu-B*08 + RMs with Vif and Nef to elicit EC-associated CTLs, then subjected these 16 vaccinees and an additional 16 unvaccinated Mamu-B*08 + controls to repeated intrarectal SIVmac239 challenges. We then performed whole-blood transcriptomic analysis of all 32 SIVmac239-infected Mamu-B*08 + RMs and eight SIVmac239-infected Mamu-B*08 – RMs during the first 14 days of infection. Results: Vaccination did not provide protection against acquisition, but peak and setpoint viremia were significantly lower in vaccinees relative to controls. We did not identify any meaningful correlations between vaccine-induced CTL parameters and SIVmac239 acquisition rate or chronic-phase viral loads. Ultimately, 13 of 16 vaccinees (81%) and 7 of 16 controls (44%) became ECs (viremia ≤ 10,000 vRNA copies/mL plasma for ≥ 4 weeks). We identified subsets of immunomodulatory genes differentially expressed (DE) between RM groupings based on vaccination status, EC status, and MHC class I genotype. These DE genes function in multiple innate immune processes, including the complement system, cytokine/chemokine signaling, pattern recognition receptors, and interferon-mediated responses. Discussion: A striking difference in the kinetics of differential gene expression among our RM groups suggests that Mamu-B*08 -associated elite control is characterized by a robust, rapid innate immune response that quickly resolves. These findings indicate that, despite the association between MHC class I genotype and elite control, innate immune factors in hyperacute SIV infection preceding CTL response development may facilitate the establishment of the EC phenotype. [ABSTRACT FROM AUTHOR]

Human Immunodeficiency Virus (HIV) is widely acknowledged for its profound impact on the immune system. Although HIV primarily affects peripheral CD4 T cells, its influence on the central nervous system (CNS) cannot be overlooked. Within the brain, microglia and CNS-associated macrophages (CAMs) serve as the primary targets for HIV and the simian immunodeficiency virus (SIV) in nonhuman primates. This infection can lead to neurological effects and establish a viral reservoir. Given the gaps in our understanding of how these cells respond in vivo to acute CNS infection, we conducted single-cell RNA sequencing (scRNA-seq) on myeloid cells from the brains of three rhesus macaques 12 days after SIV infection, along with three uninfected controls. Our analysis revealed six distinct microglial clusters including homeostatic microglia, preactivated microglia, and activated microglia expressing high levels of inflammatory and disease-related molecules. In response to acute SIV infection, the homeostatic and preactivated microglia population decreased, while the activated and disease-related microglia increased. All microglial clusters exhibited upregulation of MHC class I molecules and interferon-related genes, indicating their crucial roles in defending against SIV during the acute phase. All microglia clusters also upregulated genes linked to cellular senescence. Additionally, we identified two distinct CAM populations: CD14lowCD16hi and CD14hiCD16low CAMs. Interestingly, during acute SIV infection, the dominant CAM population changed to one with an inflammatory phenotype. Specific upregulated genes within one microglia and one macrophage cluster were associated with neurodegenerative pathways, suggesting potential links to neurocognitive disorders. This research sheds light on the intricate interactions between viral infection, innate immune responses, and the CNS, providing valuable insights for future investigations. Author summary: HIV's entry into the central nervous system (CNS) can lead to neurological dysfunction, including HIV-associated neurocognitive disorders (HAND) and the establishment of a viral reservoir. While microglia and CNS-associated macrophages (CAMs) are the primary targets of HIV in the CNS, their responses during acute HIV infection remain poorly defined. To address this, we employed the scRNA-seq technique to study microglial and CAM populations in rhesus macaques during acute SIV infection. By identifying signature genes associated with different phenotypes and mapping them to various biological and pathological pathways, we discovered two myeloid cell clusters strongly linked to neurodegenerative disorders. Other clusters were associated with inflammatory pathways, suggesting varying degrees of activation among different myeloid cell populations in the brain, possibly mediated by distinct signaling pathways. All microglia clusters developed signs of the cellular senescence pathway. These findings shed light on the immunological and pathological effects of different myeloid phenotypes in the brain during acute SIV infection, providing valuable insights for future therapeutic strategies targeting this critical stage and aiming to eliminate the viral reservoir. [ABSTRACT FROM AUTHOR]

Simian immunodeficiency virus (SIV) vaccines based upon 68-1 Rhesus Cytomegalovirus (RhCMV) vectors show remarkable protection against pathogenic SIVmac239 challenge. Across multiple independent rhesus macaque (RM) challenge studies, nearly 60% of vaccinated RM show early, complete arrest of SIVmac239 replication after effective challenge, whereas the remainder show progressive infection similar to controls. Here, we performed viral sequencing to determine whether the failure to control viral replication in non-protected RMs is associated with the acquisition of viral escape mutations. While low level viral mutations accumulated in all animals by 28 days-post-challenge, which is after the establishment of viral control in protected animals, the dominant circulating virus in virtually all unprotected RMs was nearly identical to the challenge stock, and there was no difference in mutation patterns between this cohort and unvaccinated controls. These data definitively demonstrate that viral mutation does not explain lack of viral control in RMs not protected by RhCMV/SIV vaccination. We further demonstrate that during chronic infection RhCMV/SIV vaccinated RMs do not acquire escape mutation in epitopes targeted by RhCMV/SIV, but instead display mutation in canonical MHC-Ia epitopes similar to unvaccinated RMs. This suggests that after the initial failure of viral control, unconventional T cell responses induced by 68-1 RhCMV/SIV vaccination do not exert strong selective pressure on systemically replicating SIV. [ABSTRACT FROM AUTHOR]

The effects of immunodeficiency associated with chronic HIV infection on COVID-19 disease and viral persistence have not been directly addressed in a controlled setting. In this pilot study, we exposed two pigtail macaques (PTMs) chronically infected with SIVmac239, exhibiting from very low to no CD4 T cells across all compartments, to SARS-CoV-2. We monitored the disease progression, viral replication, and evolution, and compared these outcomes with SIV-naïve PTMs infected with SARS-CoV-2. No overt signs of COVID-19 disease were observed in either animal, and the SARS-CoV-2 viral kinetics and evolution in the SIVmac239 PTMs were indistinguishable from those in the SIV-naïve PTMs in all sampled mucosal sites. However, the single-cell RNA sequencing of bronchoalveolar lavage cells revealed an infiltration of functionally inert monocytes after SARS-CoV-2 infection. Critically, neither of the SIV-infected PTMs mounted detectable anti-SARS-CoV-2 T-cell responses nor anti-SARS-CoV-2 binding or neutralizing antibodies. Thus, HIV-induced immunodeficiency alone may not be sufficient to drive the emergence of novel viral variants but may remove the ability of infected individuals to mount adaptive immune responses against SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Objectives Surface the urgent dilemma that healthcare delivery organizations (HDOs) face navigating the US Food and Drug Administration (FDA) final guidance on the use of clinical decision support (CDS) software. Materials and Methods We use sepsis as a case study to highlight the patient safety and regulatory compliance tradeoffs that 6129 hospitals in the United States must navigate. Results Sepsis CDS remains in broad, routine use. There is no commercially available sepsis CDS system that is FDA cleared as a medical device. There is no public disclosure of an HDO turning off sepsis CDS due to regulatory compliance concerns. And there is no public disclosure of FDA enforcement action against an HDO for using sepsis CDS that is not cleared as a medical device. Discussion and Conclusion We present multiple policy interventions that would relieve the current tension to enable HDOs to utilize artificial intelligence to improve patient care while also addressing FDA concerns about product safety, efficacy, and equity. [ABSTRACT FROM AUTHOR]

The capacity of HIV-1 to replicate during optimal antiretroviral therapy (ART) is challenging to assess directly. To gain greater sensitivity to detect evolution on ART, we used a nonhuman primate (NHP) model providing precise control over the level of pre-ART evolution and more comprehensive analyses than are possible with clinical samples. We infected 21 rhesus macaques (RMs) with the barcoded virus SIVmac239M and initiated ART early to minimize baseline genetic diversity. RMs were treated for 285–1200 days. We used several tests of molecular evolution to compare 1352 near-full-length (nFL) SIV DNA single genome sequences from PBMCs, lymph nodes, and spleen obtained near the time of ART initiation and those present after long-term ART, none of which showed significant changes to the SIV DNA population during ART in any animal. To investigate the possibility of ongoing replication in unsampled putative tissue sanctuaries during ART, we discontinued treatment in four animals and confirmed that none of the 336 nFL SIV RNA sequences obtained from rebound plasma viremia showed evidence of evolution. The rigorous nature of our analyses reinforced the emerging consensus of a lack of appreciable ongoing replication on effective ART and validates the relevance of this NHP model for cure studies. Precluding continued HIV-1 replication during antiretroviral therapy (ART) is critical for the design of curative strategies. Using a SIV rhesus macaque model to increase sensitivity of detection, the authors here demonstrate a lack of ongoing replication on ART. [ABSTRACT FROM AUTHOR]

The chirality-flow formalism, combined with good choices of gauge reference vectors, simplifies tree-level calculations to the extent that it is often possible to write down amplitudes corresponding to Feynman diagrams immediately. It has also proven to give a very sizable speedup in a proof of concept implementation of massless tree-level QED in MadGraph5_aMC@NLO. In the present paper we extend this analysis to QCD, including massive quarks. We define helicity-dependent versions of the gluon vertices, derive constraints on the spinor structure of propagating gluons, and explore the Schouten identity to simplify the four-gluon vertex further. For massive quarks, the chirality-flow formalism sheds light on how to exploit the freedom to measure spin along any direction to shorten the calculations. Overall, this results in a clear speedup for treating the Lorentz structure at high multiplicities. [ABSTRACT FROM AUTHOR]

Fc-mediated antibody effector functions, such as antibody-dependent cellular cytotoxicity (ADCC), can contribute to the containment HIV-1 replication but whether such activities are sufficient for protection is unclear. We previously identified an antibody to the variable 2 (V2) apex of the HIV-1 Env trimer (PGT145) that potently directs the lysis of SIV-infected cells by NK cells but poorly neutralizes SIV infectivity. To determine if ADCC is sufficient for protection, separate groups of six rhesus macaques were treated with PGT145 or a control antibody (DEN3) by intravenous infusion followed five days later by intrarectal challenge with SIVmac239. Despite high concentrations of PGT145 and potent ADCC activity in plasma on the day of challenge, all animals became infected and viral loads did not differ between the PGT145- and DEN3-treated animals. To determine if PGT145 can protect against a neutralization-sensitive virus, two additional groups of six macaques were treated with PGT145 and DEN3 and challenged with an SIVmac239 variant with a single amino acid change in Env (K180S) that increases PGT145 binding and renders the virus susceptible to neutralization by this antibody. Although there was no difference in virus acquisition, peak and chronic phase viral loads were significantly lower and time to peak viremia was significantly delayed in the PGT145-treated animals compared to the DEN3-treated control animals. Env changes were also selected in the PGT145-treated animals that confer resistance to both neutralization and ADCC. These results show that ADCC is not sufficient for protection by this V2-specific antibody. However, protection may be achieved by increasing the affinity of antibody binding to Env above the threshold required for neutralization. Author summary: Antibodies that bind to the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) on virions can neutralize viral infectivity. Antibodies may also bind to Env on the surface of virus-infected cells and recruit immune cells to eliminate the productively infected cells through a process known as antibody dependent cellular cytotoxicity (ADCC). In rare instances, certain antibodies are capable of mediating ADCC despite negligible neutralizing activity. Such antibodies are thought to have contributed to the modest protection observed in the RV144 HIV-1 vaccine trial and in some nonhuman primate studies. One antibody, PGT145, was found to cross-react with simian immunodeficiency virus (SIV) and to mediate potent ADCC against SIV-infected cells despite weak neutralization of viral infectivity. We therefore tested if the potent ADCC activity of PGT145 could protect rhesus macaques against mucosal challenge with pathogenic SIV. PGT145 did not protect against wild-type SIVmac239, but did protect against an SIVmac239 variant with a single amino acid substitution in Env (K180S) that increases antibody binding to Env and makes the virus susceptible to neutralization. Thus, while ADCC may contribute to protection against immunodeficiency viruses through the elimination of productively infected cells, the higher affinity of Env binding necessary for potent neutralization is a critical determinant of antibody-mediated protection. [ABSTRACT FROM AUTHOR]

Rereading Toni Morrison's novel Beloved , this article explores how Morrison's work at the limits of language performs the haunting ties between the Reconstruction era and the present day by offering readers a way to experience a rememory of their own. By repeatedly emphasizing the inadequacy of language in expressing traumatic experience, Beloved encourages its readers to, like its characters, look beyond language and seek out a kind of ineffable, embodied knowledge to better understand the lingering traumas of slavery. Through Morrison's concept of "invisible ink," which points to the inevitability that lived experience cannot be captured in language by the author alone but must be filled in by an active reader, this article makes a larger argument: that Beloved acts as both an invitation and a guide to read the ghostly, invisible ink of history that exists outside the novel, haunting our world itself. [ABSTRACT FROM AUTHOR]

The rebound-competent viral reservoir, composed of a virus that is able to persist during antiretroviral therapy (ART) and mediate reactivation of systemic viral replication and rebound viremia after ART interruption (ATI), remains the biggest obstacle to treating HIV infection. A better understanding of the cellular and tissue origins and the dynamics of viral populations that initiate rebound upon ATI could help develop therapeutic strategies for reducing the rebound-competent viral reservoir. In this study, barcoded simian immunodeficiency virus (SIV), SIVmac239M, was used to infect rhesus macaques to enable monitoring of viral barcode clonotypes contributing to virus detectable in plasma after ATI. Blood and tissues from secondary lymphoid organs (spleen, mesenteric lymph nodes, and inguinal lymph nodes) and from the colon, ileum, lung, liver, and brain were analyzed using viral barcode sequencing, intact proviral DNA assay, single-cell RNA sequencing, and combined CODEX and RNAscope in situ hybridization. Four of seven animals had viral barcodes detectable by deep sequencing of plasma at necropsy, although plasma viral RNA remained below 22 copies per milliliter. Among the tissues studied, mesenteric lymph nodes, inguinal lymph nodes, and spleen contained viral barcodes detected in plasma. CD4+ T cells were the main cell type harboring viral RNA after ATI. Furthermore, T cell zones in lymphoid tissues showed higher viral RNA abundance than B cell zones for most animals. These findings are consistent with lymphoid tissues contributing to the virus present in plasma early after ATI. Editor's summary: A major hurdle to treating HIV is the continued presence of the rebound-competent viral reservoir, which persists during antiretroviral therapy (ART) and serves as a source of viremia during ART interruption (ATI). Here, Solis-Leal et al. infected rhesus macaques with a barcoded strain of simian immunodeficiency virus, SIVmac239M, that enabled tracking of viral clonotypes over time and between tissues. The macaques underwent two separate ATIs, and the authors compared barcodes present in the blood and tissues 1 week after ATI. The authors found that the re-emerged viral clonotypes in plasma at ATI-2 mainly overlapped with those found in the secondary lymphoid tissues such as the spleen and lymph nodes; they also found that CD4+ T cells harbored the most viral RNA after ATI. These data suggest that secondary lymphoid organs are likely the primary viral reservoir driving rebound early after ATI. —Courtney Malo [ABSTRACT FROM AUTHOR]

Virologic suppression with antiretroviral therapy (ART) has significantly improved health outcomes for people living with HIV, yet challenges related to chronic inflammation in the central nervous system (CNS)—known as Neuro-HIV- persist. As primary targets for HIV-1 with the ability to survey and populate the CNS and interact with myeloid cells to co-ordinate neuroinflammation, CD4 T cells are pivotal in Neuro-HIV. Despite their importance, our understanding of CD4 T cell distribution in virus-targeted CNS tissues, their response to infection, and potential recovery following initiation of ART remain limited. To address these gaps, we studied ten SIVmac251-infected rhesus macaques using an ART regimen simulating suboptimal adherence. We evaluated four macaques during the acute phase pre-ART and six during the chronic phase. Our data revealed that HIV target CCR5+ CD4 T cells inhabit both the brain parenchyma and adjacent CNS tissues, encompassing choroid plexus stroma, dura mater, and the skull bone marrow. Aligning with the known susceptibility of CCR5+ CD4 T cells to viral infection and their presence within the CNS, high levels of viral RNA were detected in the brain parenchyma and its border tissues during acute SIV infection. Single-cell RNA sequencing of CD45+ cells from the brain revealed colocalization of viral transcripts within CD4 clusters and significant activation of antiviral molecules and specific effector programs within T cells, indicating CNS CD4 T cell engagement during infection. Acute infection led to marked imbalance in the CNS CD4/CD8 ratio which persisted into the chronic phase. These observations underscore the functional involvement of CD4 T cells within the CNS during SIV infection, enhancing our understanding of their role in establishing CNS viral presence. Our findings offer insights for potential T cell-focused interventions while underscoring the challenges in eradicating HIV from the CNS, particularly in the context of sub-optimal ART. Author summary: Antiretroviral therapy (ART) has improved health outcomes of people living with HIV. However, there are still challenges, especially in the central nervous system (CNS), where ongoing inflammation can lead to neurological disorders. Our study focused on understanding the role of CD4 T cells in the brain during HIV infection and sub-optimal treatment adherence. We used a model with SIV-infected rhesus monkeys to study the AIDS virus in the brain and surrounding tissues. We discovered that a subset of CD4 T cells, which are vulnerable to HIV, are present throughout the CNS. During the early stages of infection, we noticed high levels of the virus in both the brain and nearby tissues. By examining these CD4 T cells at a single-cell level, we found that they actively respond to the virus by initiating specific antiviral effector functions to fight it. Overall, our study helps us understand the role of CD4 T cells within the CNS during both acute and chronic HIV infection. This knowledge could help us develop new ways to target the virus in the CNS and devise treatments for complications related to Neuro-HIV. [ABSTRACT FROM AUTHOR]

Human immunodeficiency virus 1 (HIV-1) infection is initiated by binding of the viral envelope glycoprotein (Env) to the cell-surface receptor CD41–4. Although high-resolution structures of Env in a complex with the soluble domains of CD4 have been determined, the binding process is less understood in native membranes5–13. Here we used cryo-electron tomography to monitor Env–CD4 interactions at the membrane–membrane interfaces formed between HIV-1 and CD4-presenting virus-like particles. Env–CD4 complexes organized into clusters and rings, bringing the opposing membranes closer together. Env–CD4 clustering was dependent on capsid maturation. Subtomogram averaging and classification revealed that Env bound to one, two and finally three CD4 molecules, after which Env adopted an open state. Our data indicate that asymmetric HIV-1 Env trimers bound to one and two CD4 molecules are detectable intermediates during virus binding to host cell membranes, which probably has consequences for antibody-mediated immune responses and vaccine immunogen design.HIV-1 Env trimers bound to one, two and three CD4 molecules are observed at membrane–membrane interfaces between HIV-1 and CD4-decorated virus-like particles. [ABSTRACT FROM AUTHOR]

People living with HIV face multiple psychosocial challenges. In a large, predominantly rural Ethiopian region, 1799 HIV patients new to care were enrolled from 32 sites in a cluster randomized trial using trained community support workers with HIV to provide individual health education, counseling and social support. Participants received annual surveys through 36 months using items drawn from the Centre for Epidemiologic Studies Depression Scale-10, Medical Outcome Study Social Support Survey, and HIV/AIDS Stigma Instrument-PLWA. At 12 months (using linear mixed effects regression models controlling for enrollment site clustering), intervention participants had greater emotional/informational and tangible assistance social support scores, and lower scores assessing depression symptoms and negative self-perception due to HIV status. A significant treatment effect at 36 months was also seen on scores assessing emotional/informational social support, depression symptoms, and internalized stigma. An intervention using peer community support workers with HIV to provide individualized informational and psychological support had a positive impact on the emotional health of people living with HIV who were new to care. (ClinicalTrials.gov protocol ID: 1410S54203, May 19, 2015). [ABSTRACT FROM AUTHOR]

Frozen sections are a useful pathologic tool, but variable image quality may impede the use of artificial intelligence and machine learning in their interpretation. We aimed to identify the current research on machine learning models trained or tested on frozen section images. We searched PubMed and Web of Science for articles presenting new machine learning models published in any year. Eighteen papers met all inclusion criteria. All papers presented at least one novel model trained or tested on frozen section images. Overall, convolutional neural networks tended to have the best performance. When physicians were able to view the output of the model, they tended to perform better than either the model or physicians alone at the tested task. Models trained on frozen sections performed well when tested on other slide preparations, but models trained on only formalin‐fixed tissue performed significantly worse across other modalities. This suggests not only that machine learning can be applied to frozen section image processing, but also use of frozen section images may increase model generalizability. Additionally, expert physicians working in concert with artificial intelligence may be the future of frozen section histopathology. [ABSTRACT FROM AUTHOR]

Background: The emergence of genetic variants of SARS-CoV-2 was associated with changing epidemiological characteristics throughout coronavirus disease 2019 (COVID-19) pandemic in population-based studies. Individual-level data on the clinical characteristics of infection with different SARS-CoV-2 variants in African countries is less well documented. Objectives: To describe the evolving clinical differences observed with the various SARS-CoV-2 variants of concern and compare the Omicron-driven wave in infections to the previous Delta-driven wave. Method: We performed a retrospective observational cohort study among patients admitted to a South African referral hospital with COVID-19 pneumonia. Patients were stratified by epidemiological wave period, and in a subset, the variants associated with each wave were confirmed by genomic sequencing. Outcomes were analysed by Cox proportional hazard models. Results: We included 1689 patients were included, representing infection waves driven predominantly by ancestral, Beta, Delta and Omicron BA1/BA2 & BA4/BA5 variants. Crude 28-day mortality was 25.8% (34/133) in the Omicron wave period versus 37.1% (138/374) in the Delta wave period (hazard ratio [HR] 0.68 [95% CI 0.47–1.00] p = 0.049); this effect persisted after adjustment for age, gender, HIV status and presence of cardiovascular disease (adjusted HR [aHR] 0.43 [95% CI 0.28–0.67] p < 0.001). Hospital-wide SARS-CoV-2 admissions and deaths were highest during the Delta wave period, with a decoupling of SARS-CoV-2 deaths and overall deaths thereafter. Conclusion: There was lower in-hospital mortality during Omicron-driven waves compared with the prior Delta wave, despite patients admitted during the Omicron wave being at higher risk. Contribution: This study summarises clinical characteristics associated with SARS-CoV-2 variants during the COVID-19 pandemic at a South African tertiary hospital, demonstrating a waning impact of COVID-19 on healthcare services over time despite epidemic waves driven by new variants. Findings suggest the absence of increasing virulence from later variants and protection from population and individual-level immunity. [ABSTRACT FROM AUTHOR]

In this paper, we present an extension of MadGraph5_aMC@NLO which is able to evaluate tree-level QCD matrix-elements up to 2 → 6 (one more particle than before). To achieve this, we implemented Berends–Giele-like recursion, and re-implemented the way colour is computed such that we can now expand the colour matrix in powers of 1 / N c and truncate this expansion to a chosen order. For high multiplicity samples, even without truncating the colour matrix, the new implementation offers a speed gain compared to the previous MadGraph5_aMC@NLO code. [ABSTRACT FROM AUTHOR]

Retention in care is a major challenge for global AIDS control, including sub-Saharan Africa. In a large Ethiopian region, we evaluated an intervention where HIV positive community support workers (CSWs) provided HIV health education, personal counseling and social support for HIV patients new to care. We enrolled 1,799 patients recently entering care from 32 hospitals and health centers, randomized to intervention or control sites. Dates of all clinic visits, plus deaths or transfers were abstracted from HIV medical records. Primary outcomes were gap in clinical care (>90 days from a missed clinical or drug pickup appointment) and death. For 36 months of follow-up, and for the first 12 months after enrollment, weighted risk differences [RD] between treatment arms were modest and non-significant for gap in clinical care, death or either outcome. Through 36 months, 624 of 980 controls and 469 of 819 intervention participants had gaps in clinical care (RD = −5.5%, 95% confidence interval [CI] = −17.9%, 7.0%); 79 controls and 82 intervention participants died (RD = 2.5% 95% CI = −1.7%, 6.8%). Factors including HIV stigma and a volatile political climate may have attenuated the advantages we anticipated, demonstrating how benefits of CSW interventions may depend upon psychosocial, clinical and structural factors particular to specific community settings. [ABSTRACT FROM AUTHOR]

SIVmac239 infection of macaques is a favored model of human HIV infection. However, the SIVmac239 envelope (Env) trimer structure, glycan occupancy, and the targets and ability of neutralizing antibodies (nAbs) to protect against SIVmac239 remain unknown. Here, we report the isolation of SIVmac239 nAbs that recognize a glycan hole and the V1/V4 loop. A high-resolution structure of a SIVmac239 Env trimer-nAb complex shows many similarities to HIV and SIVcpz Envs, but with distinct V4 features and an extended V1 loop. Moreover, SIVmac239 Env has a higher glycan shield density than HIV Env that may contribute to poor or delayed nAb responses in SIVmac239-infected macaques. Passive transfer of a nAb protects macaques from repeated intravenous SIVmac239 challenge at serum titers comparable to those described for protection of humans against HIV infection. Our results provide structural insights for vaccine design and shed light on antibody-mediated protection in the SIV model. SIVmac239 infection of macaques is a favored model of human HIV infection, but antibody-mediated protection for SIVmac239 is insufficiently understood. Here, Zhao and Berndsen et al isolated nAbs and confirmed protection against SIVmac239 infection in passive transfer studies in macaques. The nAb was used to provide the first high-resolution structure of a rhesus SIV trimer by CryoEM. Analysis of the glycosylation pattern of this SIV trimer suggests a denser glycan shield on Env for rhesus SIV compared to chimpanzee SIV or HIV-1, which partially explains the poor nAb response of rhesus macaques to SIVmac239 infection. [ABSTRACT FROM AUTHOR]

Antiretroviral therapy (ART) is not curative due to the persistence of a reservoir of HIV-infected cells, particularly in tissues such as lymph nodes, with the potential to cause viral rebound after treatment cessation. In this study, fingolimod (FTY720), a lysophospholipid sphingosine-1-phosphate receptor modulator is administered to SIV-infected rhesus macaques at initiation of ART to block the egress from lymphoid tissues of natural killer and T-cells, thereby promoting proximity between cytolytic cells and infected CD4+ T-cells. When compared with the ART-only controls, FTY720 treatment during the initial weeks of ART induces a profound lymphopenia and increases frequencies of CD8+ T-cells expressing perforin in lymph nodes, but not their killing capacity; FTY720 also increases frequencies of cytolytic NK cells in lymph nodes. This increase of cytolytic cells, however, does not limit measures of viral persistence during ART, including intact proviral genomes. After ART interruption, a subset of animals that initially receives FTY720 displays a modest delay in viral rebound, with reduced plasma viremia and frequencies of infected T follicular helper cells. Further research is needed to optimize the potential utility of FTY720 when coupled with strategies that boost the antiviral function of T-cells in lymphoid tissues. Although antiretroviral therapy (ART) is able to successfully suppress plasma viremia in most people living with HIV, ART withdrawal typically results in viral replication and rebound. Authors investigate the effect, in terms of delay in viral replication, and immune cell dynamics in lymphoid tissue, of fingolimod (FTY720) administration at the time of ART initiation in SIV-infected rhesus macaques. [ABSTRACT FROM AUTHOR]

The HIV/SIV envelope glycoprotein (Env) cytoplasmic domain contains a highly conserved Tyr-based trafficking signal that mediates both clathrin-dependent endocytosis and polarized sorting. Despite extensive analysis, the role of these functions in viral infection and pathogenesis is unclear. An SIV molecular clone (SIVmac239) in which this signal is inactivated by deletion of Gly-720 and Tyr-721 (SIVmac239ΔGY), replicates acutely to high levels in pigtail macaques (PTM) but is rapidly controlled. However, we previously reported that rhesus macaques and PTM can progress to AIDS following SIVmac239ΔGY infection in association with novel amino acid changes in the Env cytoplasmic domain. These included an R722G flanking the ΔGY deletion and a nine nucleotide deletion encoding amino acids 734–736 (ΔQTH) that overlaps the rev and tat open reading frames. We show that molecular clones containing these mutations reconstitute signals for both endocytosis and polarized sorting. In one PTM, a novel genotype was selected that generated a new signal for polarized sorting but not endocytosis. This genotype, together with the ΔGY mutation, was conserved in association with high viral loads for several months when introduced into naïve PTMs. For the first time, our findings reveal strong selection pressure for Env endocytosis and particularly for polarized sorting during pathogenic SIV infection in vivo. Author summary: In the cytoplasmic domain (CD) of their envelope glycoproteins (Env), all human and simian immunodeficiency viruses (HIV and SIV) have a tyrosine-dependent motif that is a potent signal for Env endocytosis and polarized sorting in infected cells. The role and relevance of this trafficking signal in pathogenesis is unknown. For a pathogenic SIV, we have shown that deletion of this tyrosine and a preceding glycine, creating a virus termed ΔGY, results in profoundly altered pathogenesis in pigtail macaques. Viral replication is rapidly suppressed, systemic immune activation fails to occur, and CD4 cells are spared. However, although uncommon, ΔGY-infected macaques can develop high viral loads and disease in association with novel mutations in the Env CD. Here we show that these mutations restore trafficking functions, remarkably, at the expense of tat and rev genes in overlapping reading frames. We quantified the effects of these new signals and demonstrated their ability to confer high viral loads and/or disease to ΔGY-infected animals. These findings demonstrate strong in vivo selection pressures to maintain Env trafficking, in particular, polarized sorting. We present hypotheses for why this long recognized, but poorly understood Env function is conserved and essential for HIV/SIV pathogenesis. [ABSTRACT FROM AUTHOR]

Recently we introduced the chirality-flow formalism, a method which builds on the spinor-helicity formalism and is inspired by the color-flow idea in QCD. With this formalism, Feynman rules and diagrams are simplified to the extent that it is often possible to immediately, by hand, write down a helicity amplitude given a Feynman diagram. In this paper we show that the method can also speed up numerical evaluation of scattering amplitudes by considering e + e - going to n photons in a MadGraph-based tree-level implementation. We find that the computation time is reduced by roughly a factor ten for six photons, and that it scales better with the number of external particles than the default MadGraph5_aMC@NLO implementation. This performance gain is in part attributed to the more compact Lorentz structures involved, and in part due to a transparent choice of gauge reference vectors which reduces the number of Feynman diagrams considered. [ABSTRACT FROM AUTHOR]

Background: Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) spreads rapidly amongst residents of skilled nursing facilities (SNFs). The rapid transmission dynamics and high morbidity and mortality that occur in SNFs emphasize the need for early detection of cases. We hypothesized that residents of SNFs infected with SARS‐CoV‐2 would demonstrate an acute change in either temperature or oxygen saturation (SpO2) prior to symptom onset. The Minnesota Department of Health (MDH) conducted a retrospective analysis of both temperature and SpO2 at two separate SNFs to assess the utility of these quantitative markers to identify SARS‐CoV‐2 infection prior to the development of symptoms. Methods: A retrospective analysis was conducted of 165 individuals positive for SARS‐CoV‐2 who were residents of SNFs that experienced coronavirus disease 2019 (COVID‐19) outbreaks during April–June 2020 in a metropolitan area of Minnesota. Age, sex, symptomology, temperature and SpO2 values, date of symptom onset, and date of positive SARS‐CoV‐2 test were analyzed. Temperature and SpO2 values for the period 14 days before and after the date of initial positive test were included. Descriptive analyses evaluated changes in temperature and SpO2, defined as either exceeding a set threshold or demonstrating an acute change between consecutive measurements. Results: Two (1%) residents had a temperature value ≥100°F, and 30 (18%) had at least one value ≥99°F within 14 days before symptom development. One hundred and sixteen residents (70%) had at least one SpO2 value ≤94%, while 131 (80%) had an acute decrease in SpO2 of ≥3% between consecutive values in the 14 days prior to symptom onset. Conclusions: Our results suggest that acute change in SpO2 might be useful in the identification of SARS‐CoV‐2 infection prior to the development of symptoms among residents living in SNFs. Facilities may consider adding SpO2 to daily temperature and symptom screening checklists to improve early detection of residents of SNFs infected with SARS‐CoV‐2. [ABSTRACT FROM AUTHOR]

In people living with HIV (PLWH) on antiretroviral therapy (ART), virus persists in a latent form where there is minimal transcription or protein expression. Latently infected cells are a major barrier to curing HIV. Increasing HIV transcription and viral production in latently infected cells could facilitate immune recognition and reduce the pool of infected cells that persist on ART. Given that programmed cell death protein 1 (PD-1) expressing CD4+ T cells are preferentially infected with HIV in PLWH on ART, we aimed to determine whether administration of antibodies targeting PD-1 would reverse HIV latency in vivo. We therefore evaluated the impact of intravenous administration of pembrolizumab every 3 weeks on HIV latency in 32 PLWH and cancer on ART. After the first infusion of anti–PD-1, we observed a median 1.32-fold increase in unspliced HIV RNA and 1.61-fold increase in unspliced RNA:DNA ratio in sorted blood CD4+ T cells compared to baseline. We also observed a 1.65-fold increase in plasma HIV RNA. The frequency of CD4+ T cells with inducible virus evaluated using the tat/rev limiting dilution assay was higher after 6 cycles compared to baseline. Phylogenetic analyses of HIV env sequences in a participant who developed low concentrations of HIV viremia after 6 cycles of pembrolizumab did not demonstrate clonal expansion of HIV-infected cells. These data are consistent with anti–PD-1 being able to reverse HIV latency in vivo and support the rationale for combining anti–PD-1 with other interventions to reduce the HIV reservoir. PD-1 blockade for HIV: Strategies to target and reverse the latent HIV reservoir are required to cure HIV. Because CD4+ T cells expressing programmed cell death protein 1 (PD-1) are preferentially infected with HIV in an individual on antiretroviral therapy, PD-1 is an attractive target to manipulate the latent reservoir. To this end, Uldrick et al. measured the impact of anti–PD-1 treatment with pembrolizumab on the HIV reservoir in 32 individuals living with HIV on suppressive antiretroviral therapy and diagnosed with cancer. They observed evidence of increased unspliced HIV RNA and of the unspliced RNA:DNA ratio, consistent with anti–PD-1 treatment having the potential to reverse HIV latency. Further studies are needed to evaluate the dose and frequency of anti–PD-1 treatment required for latency reversal. [ABSTRACT FROM AUTHOR]

Activation of the NF-κB signaling pathway by Protein Kinase C (PKC) agonists is a potent mechanism for human immunodeficiency virus (HIV) latency disruption in vitro. However, significant toxicity risks and the lack of evidence supporting their activity in vivo have limited further evaluation of PKC agonists as HIV latency-reversing agents (LRA) in cure strategies. Here we evaluated whether GSK445A, a stabilized ingenol-B derivative, can induce HIV/simian immunodeficiency virus (SIV) transcription and virus production in vitro and demonstrate pharmacological activity in nonhuman primates (NHP). CD4+ T cells from people living with HIV and from SIV+ rhesus macaques (RM) on antiretroviral therapy (ART) exposed in vitro to 25 nM of GSK445A produced cell-associated viral transcripts as well as viral particles at levels similar to those induced by PMA/Ionomycin, indicating that GSK445A can potently reverse HIV/SIV latency. Importantly, these concentrations of GSK445A did not impair the proliferation or survival of HIV-specific CD8+ T cells, but instead, increased their numbers and enhanced IFN-γ production in response to HIV peptides. In vivo, GSK445A tolerability was established in SIV-naïve RM at 15 μg/kg although tolerability was reduced in SIV-infected RM on ART. Increases in plasma viremia following GSK445A administration were suggestive of increased SIV transcription in vivo. Collectively, these results indicate that GSK445A is a potent HIV/SIV LRA in vitro and has a tolerable safety profile amenable for further evaluation in vivo in NHP models of HIV cure/remission. Author summary: Antiretroviral therapy (ART) is not a definitive cure HIV infection, in part, because the virus is able to integrate its genetic material in the host cell and remain in a dormant but fully replication-competent form during ART. These latently-infected cells can persist for long periods of time and remain hidden from the host's immune system. If ART is stopped, the virus can reactivate from this pool of infected cells and resume HIV replication and disease progression. As such, finding and eliminating cells with latent HIV infection is priority for HIV cure research. One approach is to use compounds referred to as latency-reversing agents, that can induce HIV reactivation during ART. The goal of this approach is to facilitate elimination of infected cells by the virus itself once it reactivates or by the host's immune system, once virus induction renders the cells detectable by the immune system, while also preventing the virus from infecting new cells due to the continued presence of ART. In this study we report on the activity of a novel latency-reversing agent called GSK445A, a potent activator of the enzyme protein kinase C (PKC). We show that GSK445A can induce HIV and simian immunodeficiency virus (SIV) latency reversal in vitro and has a tolerable saftey profile in nonhuman primates that should permit further testing of this PKC-agonist in strategies to cure HIV. [ABSTRACT FROM AUTHOR]

Introduction: Accurate and precise platelet (PLT) count is critical for the appropriate management of patients with thrombocytopenia. This study evaluated the performance of PLT counting with the Abbott Alinity hq hematology analyzer, which utilizes multi‐dimensional optical technology. Methods: Imprecision, linearity, and accuracy were assessed per CLSI guidelines. Alinity hq PLT results were compared to the international flow cytometry reference method (IRM) in the concentration range of 6.3 to 103.0 × 109/L. Additional comparisons were made with Sysmex XN‐3000 PLT counts: impedance (PLT‐I), optical (PLT‐O), and optical fluorescent (PLT‐F) methods. Results: The average within‐run %CV was 4.7% on patient samples with PLT concentrations ranging from 13.1 to 41.7 × 109/L, and the within‐laboratory %CV was 3.6% at the level of 68.2 × 109/L. Linearity evaluation indicated a maximum deviation of 3.1% from the linear fit in the range of 0.1 to 316.8 × 109/L. Comparison between Alinity hq and the IRM PLT counts yielded a correlation coefficient of 0.99 and predicted bias of 0.0 and −0.5 × 109/L at 10.0 and 20.0 × 109/L transfusion thresholds, respectively. Alinity hq PLT counts also correlated well with Sysmex PLT counts, with strongest correlation obtained with PLT‐F and PLT‐O (r =.99) methods. Conclusion: This study demonstrated excellent analytical performance of Alinity hq PLT counting in thrombocytopenic samples, equivalency with the IRM and strong agreement with Sysmex PLT‐F and PLT‐O methods. The Alinity hq multi‐dimensional optical PLT count is available with every CBC without additional reagents and may help promote efficiency in clinical laboratories. [ABSTRACT FROM AUTHOR]

Central retinal artery occlusion (CRAO) is a condition that causes sudden vision loss due to obstruction of the retinal artery, typically from a thrombotic or embolic source. It is often associated with atherosclerotic risk factors, including cardiovascular disease, diabetes, hyperlipidemia, and a history of cerebrovascular disease. CRAO often leads to a poor visual outcome as well as neovascularization of the iris, retina, and optic disc, which can exacerbate vision loss and cause pain. While there are several treatment modalities for CRAO, few have been proven to be effective in decreasing the effects of neovascularization. The use of hyperbaric oxygen (HBO2) therapy is often used in the treatment of CRAO due to its ease of use and relatively benign side effect profile. This study aims to assess the degree of improvement in visual acuity (VA) and neovascularization following HBO2. Our data ultimately shows that 20% of patients developed neovascularization after HBO2 compared to 29.8% of those who did not undergo HBO2 (p<.05). Our findings suggest that HBO2 has a statistically significant protective effect against neovascularization and may improve long-term visual acuity. [ABSTRACT FROM AUTHOR]

Reports from Sub-Saharan Africa, with a large HIV-infected population, vary widely in how often HIV status is disclosed to others, including spouses and other partners. We surveyed 1799 Ethiopian HIV patients newly enrolled in care within the previous 3 months at one of 32 local hospitals and health centers about disclosure of HIV status and two perceived social support domains: emotional/informational (EI) and tangible assistance (TA) support. Disclosure to another person was reported by 1389 (77%) persons. Disclosure rates to specific persons were: spouses or other partners = 74%; mothers = 24%; fathers = 16%; children = 26%; other family members = 37%; friends = 19%, and neighbors/other community members = 13%. Disclosure to another person was associated with higher social support scores on both EI and TA domains, marriage, and a longer time knowing HIV status. In multivariate adjusted models, disclosure to any person, as well as disclosure specifically to a spouse or partner, were associated with higher EI and higher TA social support scores. Provision of knowledgeable and emotionally supportive assistance can be an important factor in facilitating HIV disclosure. Helping persons with HIV decide who to disclose to and how to do so in the most positive manner is an essential component of HIV care and support. [ABSTRACT FROM AUTHOR]

Analytical treatment interruptions (ATIs) of antiretroviral therapy (ART) play a central role in evaluating the efficacy of HIV-1 treatment strategies targeting virus that persists despite ART. However, it remains unclear if ATIs alter the rebound-competent viral reservoir (RCVR), the virus population that persists during ART and from which viral recrudescence originates after ART discontinuation. To assess the impact of ATIs on the RCVR, we used a barcode sequence tagged SIV to track individual viral lineages through a series of ATIs in Rhesus macaques. We demonstrate that transient replication of individual rebounding lineages during an ATI can lead to their enrichment in the RCVR, increasing their probability of reactivating again after treatment discontinuation. These data establish that the RCVR can be altered by uncontrolled replication during ATI. Author summary: While HIV-1 replication can be effectively controlled by combination antiretroviral therapy in most individuals, it does not clear long-lived viral reservoirs that were established before ART was started. This necessitates life-long adherence to therapy to prevent re-emergence of infection. Clinical trials evaluating interventions that would allow people to safely stop ART rely on treatment interruptions to determine if, and when, viral rebound occurs. However, it remains unclear if extended viral replication during treatment interruptions can increase the size of the viral reservoir or alter its genetic composition. To directly assess the impact of replication on the viral reservoir, we used a barcoded simian immunodeficiency virus in nonhuman primates to track the reactivation and replication dynamics of individual viral lineages across a series of treatment interruptions. We found that transient replication of rebounding viral variants during an interruption increased their probability of reactivating again when treatment was subsequently discontinued. Our findings suggest that the viral reservoir can become enriched by viral lineages that are actively replicating during treatment interruptions, which could have important implications for clinical trial participants. [ABSTRACT FROM AUTHOR]

Unlike HIV infection, which progresses to AIDS absent suppressive anti-retroviral therapy, nonpathogenic infections in natural hosts, such African green monkeys, are characterized by a lack of gut microbial translocation and robust secondary lymphoid natural killer cell responses resulting in an absence of chronic inflammation and limited SIV dissemination in lymph node B-cell follicles. Here we report, using the pathogenic model of antiretroviral therapy-treated, SIV-infected rhesus macaques that sequential interleukin-21 and interferon alpha therapy generate terminally differentiated blood natural killer cells (NKG2a/clowCD16+) with potent human leukocyte antigen-E-restricted activity in response to SIV envelope peptides. This is in contrast to control macaques, where less differentiated, interferon gamma-producing natural killer cells predominate. The frequency and activity of terminally differentiated NKG2a/clowCD16+ natural killer cells correlates with a reduction of replication-competent SIV in lymph node during antiretroviral therapy and time to viral rebound following analytical treatment interruption. These data demonstrate that African green monkey-like natural killer cell differentiation profiles can be rescued in rhesus macaques to promote viral clearance in tissues. Infection of African green monkeys with SIV is associated with reduced pathogenicity. Here the authors explore the requirement of differentiated NK cell populations in a pathogenic Rhesus macaque model of SIV infection and show administration of IL-21 and IFNα rescues terminally differentiated NK cells, similarly to what found in African green monkeys, and limits the SIV reservoir in antiretroviral therapy treated macaques. [ABSTRACT FROM AUTHOR]

In a recent paper we introduced the chirality-flow formalism, a method for simple and transparent calculations of Feynman diagrams based on the left- and right-chiral sl (2 , C) nature of spacetime. While our previous work focused on massless QED and QCD at tree-level, we here extend the chirality-flow formalism to the full (tree-level) Standard Model, including massive particles and electroweak interactions – for which the W-interaction simplifies elegantly due to its chiral nature. We illustrate how values of Feynman diagrams can be immediately written down with some representative examples. [ABSTRACT FROM AUTHOR]

The antiviral properties of broadly neutralizing antibodies against HIV are well-documented but no vaccine is currently able to elicit protective titers of these responses in primates. While current vaccine modalities can readily induce non-neutralizing antibodies against simian immunodeficiency virus (SIV) and HIV, the ability of these responses to restrict lentivirus transmission and replication remains controversial. Here, we investigated the antiviral properties of non-neutralizing antibodies in a group of Indian rhesus macaques (RMs) that were vaccinated with vif , rev, tat, nef , and env , as part of a previous study conducted by our group. These animals manifested rapid and durable control of viral replication to below detection limits shortly after SIVmac239 infection. Although these animals had no serological neutralizing activity against SIVmac239 prior to infection, their pre-challenge titers of Env-binding antibodies correlated with control of viral replication. To assess the contribution of anti-Env humoral immune responses to virologic control in two of these animals, we transiently depleted their circulating antibodies via extracorporeal plasma immunoadsorption and inhibition of IgG recycling through antibody-mediated blockade of the neonatal Fc receptor. These procedures reduced Ig serum concentrations by up to 80% and temporarily induced SIVmac239 replication in these animals. Next, we transferred purified total Ig from the rapid controllers into six vaccinated RMs one day before intrarectal challenge with SIVmac239. Although recipients of the hyperimmune anti-SIV Ig fraction were not protected from infection, their peak and chronic phase viral loads were significantly lower than those in concurrent unvaccinated control animals. Together, our results suggest that non-neutralizing Abs may play a role in the suppression of SIVmac239 viremia. [ABSTRACT FROM AUTHOR]

We take a fresh look at Feynman diagrams in the spinor-helicity formalism. Focusing on tree-level massless QED and QCD, we develop a new and conceptually simple graphical method for their calculation. In this pictorial method, which we dub the chirality-flow formalism, Feynman diagrams are directly represented in terms of chirality-flow lines corresponding to spinor inner products, without the need to resort to intermediate algebraic manipulations. [ABSTRACT FROM AUTHOR]

Treatment of HIV infection with either antiretroviral (ARV) therapy or neutralizing monoclonal antibodies (NAbs) leads to a reduction in HIV plasma virus. Both ARVs and NAbs prevent new rounds of viral infection, but NAbs may have the additional capacity to accelerate the loss of virus-infected cells through Fc gamma receptor (FcγR)-mediated effector functions, which should affect the kinetics of plasma-virus decline. Here, we formally test the role of effector function in vivo by comparing the rate and timing of plasma-virus clearance in response to a single-dose treatment with either unmodified NAb or those with either reduced or augmented Fc function. When infused into viremic simian HIV (SHIV)-infected rhesus macaques, there was a 21% difference in slope of plasma-virus decline between NAb and NAb with reduced Fc function. NAb engineered to increase FcγRIII binding and improve antibody-dependent cellular cytotoxicity (ADCC) in vitro resulted in arming of effector cells in vivo, yet led to viral-decay kinetics similar to NAbs with reduced Fc function. These studies show that the predominant mechanism of antiviral activity of HIV NAbs is through inhibition of viral entry, but that Fc function can contribute to the overall antiviral activity, making them distinct from standard ARVs. [ABSTRACT FROM AUTHOR]

In QCD, we are used to describing the SU(3) color space in terms of a flow of color. At the algebra level, the Lorentz group consists of two copies of the (complexified) su(2) algebra, so one may anticipate that a similar way of thinking about the spacetime structure of scattering amplitudes should exist. In this article, we argue that this is indeed the case, and introduce the chirality-flow formalism for massless tree-level QED and QCD. Within the chirality-flow formalism, scattering amplitudes can directly be written down in terms of Lorentz-invariant spinor inner products, similar to how the color structure can be described in terms of a color flow. [ABSTRACT FROM AUTHOR]

Most simian immunodeficiency viruses use Nef to counteract the tetherin proteins of their nonhuman primate hosts. Nef also downmodulates cell-surface CD4 and MHC class I (MHC I) molecules and enhances viral infectivity by counteracting SERINC5. We previously demonstrated that tetherin antagonism by SIV Nef is genetically separable from CD4- and MHC I-downmodulation. Here we show that disruption of tetherin antagonism by Nef impairs virus replication during acute SIV infection of rhesus macaques. A combination of mutations was introduced into the SIVmac239 genome resulting in three amino acid substitutions in Nef that impair tetherin antagonism, but not CD3-, CD4- or MHC I-downmodulation. Further characterization of this mutant (SIVmac239AAA) revealed that these changes also result in partial sensitivity to SERINC5. Separate groups of four rhesus macaques were infected with either wild-type SIVmac239 or SIVmac239AAA, and viral RNA loads in plasma and sequence changes in the viral genome were monitored. Viral loads were significantly lower during acute infection in animals infected with SIVmac239AAA than in animals infected with wild-type SIVmac239. Sequence analysis of the virus population in plasma confirmed that the substitutions in Nef were retained during acute infection; however, changes were observed by week 24 post-infection that fully restored anti-tetherin activity and partially restored anti-SERINC5 activity. These observations reveal overlap in the residues of SIV Nef required for counteracting tetherin and SERINC5 and selective pressure to overcome these restriction factors in vivo. Author summary: The SIV Nef protein enhances virus replication by removing certain cellular proteins from the surface of infected cells. Whereas the downmodulation of tetherin enhances virus release from infected cells, the downmodulation of SERINC5, and to a lesser extent SERINC3, increases viral infectivity. Although these Nef-mediated effects on the host cell have been demonstrated in vitro, the relevance of these activities to virus replication in primates has not been directly assessed. We therefore introduced mutations into SIV that render Nef ineffective against tetherin and SERINC5. Rhesus macaques infected with this virus exhibited lower acute viremia compared to animals infected with wild-type SIV. We also observed a partial recovery of these functions as a result of the accumulation of compensatory mutations in Nef. This study therefore demonstrates that overcoming restriction by tetherin and SERINC5 is important for efficient replication of immunodeficiency viruses in their infected hosts. [ABSTRACT FROM AUTHOR]

Long-term delivery of anti-HIV monoclonal antibodies using adeno-associated virus (AAV) holds promise for the prevention and treatment of HIV infection. We previously reported that after receiving a single administration of AAV vector coding for anti-SIV antibody 5L7, monkey 84-05 achieved high levels of AAV-delivered 5L7 IgG1 in vivo which conferred sterile protection against six successive, escalating dose, intravenous challenges with highly infectious, highly pathogenic SIVmac239, including a final challenge with 10 animal infectious doses (1). Here we report that monkey 84-05 has successfully maintained 240–350 μg/ml of anti-SIV antibody 5L7 for over 6 years. Approximately 2% of the circulating IgG in this monkey is this one monoclonal antibody. This monkey generated little or no anti-drug antibodies (ADA) to the AAV-delivered antibody for the duration of the study. Due to the nature of the high-dose challenge used and in order to rule out a potential low-level infection not detected by regular viral loads, we have used ultrasensitive techniques to detect cell-associated viral DNA and RNA in PBMCs from this animal. In addition, we have tested serum from 84-05 by ELISA against overlapping peptides spanning the whole envelope sequence for SIVmac239 (PepScan) and against recombinant p27 and gp41 proteins. No reactivity has been detected in the ELISAs indicating the absence of naturally arising anti-SIV antibodies; moreover, the ultrasensitive cell-associated viral tests yielded no positive reaction. We conclude that macaque 84-05 was effectively protected and remained uninfected. Our data show that durable, continuous antibody expression can be achieved after one single administration of AAV and support the potential for lifelong protection against HIV from a single vector administration. [ABSTRACT FROM AUTHOR]

Anti-retroviral therapy (ART) has been highly successful in controlling HIV replication, reducing viral burden, and preventing both progression to AIDS and viral transmission. Yet, ART alone cannot cure the infection. Even after years of successful therapy, ART withdrawal leads inevitably to viral rebound within a few weeks or months. Our hypothesis: effective therapy must control both the replicating virus pool and the reactivatable latent viral reservoir. To do this, we have combined ART and immunotherapy to attack both viral pools simultaneously. The vaccine regimen consisted of DNA vaccine expressing SIV Gag, followed by a boost with live attenuated rubella/gag vectors. The vectors grow well in rhesus macaques, and they are potent immunogens when used in a prime and boost strategy. We infected rhesus macaques by high dose mucosal challenge with virulent SIVmac251 and waited three days to allow viral dissemination and establishment of a reactivatable viral reservoir before starting ART. While on ART, the control group received control DNA and empty rubella vaccine, while the immunotherapy group received DNA/gag prime, followed by boosts with rubella vectors expressing SIV gag over 27 weeks. Both groups had a vaccine "take" to rubella, and the vaccine group developed antibodies and T cells specific for Gag. Five weeks after the last immunization, we stopped ART and monitored virus rebound. All four control animals eventually had a viral rebound, and two were euthanized for AIDS. One control macaque did not rebound until 2 years after ART release. In contrast, there was only one viral rebound in the vaccine group. Three out of four vaccinees had no viral rebound, even after CD8 depletion, and they remain in drug-free viral remission more than 2.5 years later. The strategy of early ART combined with immunotherapy can produce a sustained SIV remission in macaques and may be relevant for immunotherapy of HIV in humans. [ABSTRACT FROM AUTHOR]

Background: The PD1/PD-L1 pathway contributes to the pathogenesis of human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) infection, and blockade of this pathway may have potential to restore immune function and promote viral control or elimination. In this study, we combined a checkpoint inhibitor anti-PD-L1 (Avelumab) and recombinant human interleukin-15 (rhIL-15) in SIV-infected rhesus macaques (RM).Methods: The rhIL-15 was administered as continuous infusion in 2 cycles of 10 days in the context of weekly administration of anti-PD-L1 (Avelumab) in SIV-infected RM receiving combination antiretroviral therapy (cART). Safety, immunological parameters, and viral loads were monitored during the study.Results: Administration of rhIL-15/anti-PD-L1 was safe and well tolerated. Treatment resulted in transient increases in proliferating (Ki67+) natural killer and CD8 T cells. In addition, treatment expanded a CXCR3+PD1-/low CD8 T-cell subset with the ability to secrete cytokines. Despite these effects, no changes in plasma viremia were observed after cART interruption.Conclusions: Expansion of the CXCR3+PD1-/low CD8 T-cell subset with functional capacity and potential to traffic to sites of viral reservoirs in SIV-infected rhesus macaques had no demonstrable effect on plasma viremia after cART interruption. [ABSTRACT FROM AUTHOR]

Human immunodeficiency virus (HIV) persists indefinitely in individuals with HIV who receive antiretroviral therapy (ART) owing to a reservoir of latently infected cells that contain replication-competent virus1–4. Here, to better understand the mechanisms responsible for latency persistence and reversal, we used the interleukin-15 superagonist N-803 in conjunction with the depletion of CD8+ lymphocytes in ART-treated macaques infected with simian immunodeficiency virus (SIV). Although N-803 alone did not reactivate virus production, its administration after the depletion of CD8+ lymphocytes in conjunction with ART treatment induced robust and persistent reactivation of the virus in vivo. We found viraemia of more than 60 copies per ml in all macaques (n = 14; 100%) and in 41 out of a total of 56 samples (73.2%) that were collected each week after N-803 administration. Notably, concordant results were obtained in ART-treated HIV-infected humanized mice. In addition, we observed that co-culture with CD8+ T cells blocked the in vitro latency-reversing effect of N-803 on primary human CD4+ T cells that were latently infected with HIV. These results advance our understanding of the mechanisms responsible for latency reversal and lentivirus reactivation during ART-suppressed infection. The interleukin-15 superagonist N-803, combined with the depletion of CD8+ lymphocytes, induced a robust and persistent reactivation of the virus in vivo in both antiretroviral-therapy-treated SIV-infected macaques and HIV-infected humanized mice. [ABSTRACT FROM AUTHOR]

The rapidity of replication coupled with a high mutation rate enables HIV to evade selective pressures imposed by host immune responses. Investigating the ability of HIV to escape different selection forces has generally relied on population-level measures, such as the time to detectable escape mutations in plasma and the rate these mutations subsequently take over the virus population. Here we employed a barcoded synthetic swarm of simian immunodeficiency virus (SIV) in rhesus macaques to investigate the generation and selection of escape mutations within individual viral lineages at the Mamu-A*01-restricted Tat-SL8 epitope. We observed the persistence of more than 1,000 different barcode lineages following selection after acquiring escape mutations. Furthermore, the increased resolution into the virus population afforded by barcode analysis revealed changes in the population structure of the viral quasispecies as it adapted to immune pressure. The high frequency of emergence of escape mutations in parallel viral lineages at the Tat-SL8 epitope highlights the challenge posed by viral escape for the development of T cell-based vaccines. Importantly, the level of viral replication required for generating escape mutations in individual lineages can be directly estimated using the barcoded virus, thereby identifying the level of efficacy required for a successful vaccine to limit escape. Overall, assessing the survival of barcoded viral lineages during selection provides a direct and quantitative measure of the stringency of the underlying genetic bottleneck, making it possible to predict the ability of the virus to escape selective forces induced by host immune responses as well as during therapeutic interventions. [ABSTRACT FROM AUTHOR]

The 13th sentence of the first paragraph of the Materials and Methods subsection Animals, regarding the antibiotic/antiparasitic treatment regimen, is incorrect. The authors do not believe that the differences in the antibiotic/antiparasitic treatment used prior to the study affected the results and conclusions. The correct text is: Prior to the study and as part of the facility animal management, 22 animals received an oral antibiotic/antiparasitic regimen between 1 and 10 months prior to study which included metronidazole (50 mg + 21mg/kg or 50 mg/kg once or twice daily for 5-10 days) and fenbendazole (50 mg/kg once daily for 3-5 days), with some of these animals (n = 15) also receiving enrofloxacin (10 mg/kg once daily for 7 days). [Extracted from the article]

Plasmacytoid dendritic cells (PDCs) and their production of interferon-alpha (IFN-α) are believed to play an important role in human immunodeficiency virus, type I (HIV-1) pathogenesis. PDCs produce IFN-α and other proinflammatory cytokines through stimulation of Toll-like receptor 7 (TLR7) and TLR9 present in endosomal compartments. TLR7 recognizes single-stranded viral RNA, while TLR9 recognizes unmethylated DNA. In this study, we examined the mechanisms that may underlie variations in IFN-α production in response to HIV, and the impact of these variations on HIV pathogenesis. In four distinct cohorts, we examined PDC production of IFN-α upon stimulation with inactivated HIV-1 particles and unmethylated DNA. The signaling cascade of TLR7 bifurcates at the myeloid differentiation protein 88 (MyD88) adaptor protein to induce expression of either IFN-α or TNF-α. To determine whether variations in IFN-α production are modulated at the level of the receptor complex or downstream of it, we correlated production of IFN-α and TNF-α following stimulation of TLR7 or TLR9 receptors. Flow cytometry detection of intracellular cytokines showed strong, direct correlations between IFN-α and TNF-α expression in all four cohorts, suggesting that variations in IFN-α production are not due to variations downstream of the receptor complex. We then investigated the events upstream of TLR binding by using lipid-like vesicles to deliver TLR ligands directly to the TLR receptors, bypassing the need for CD4 binding and endocytosis. Similar tight correlations were found in IFN-α and TNF-α production in response to the TLR ligands. Taken together, these results strongly suggest that differences in IFN-α production depend on the regulatory processes at the level of the TLR7 receptor complex. Additionally, we found no association between IFN-α production before HIV infection and disease progression. [ABSTRACT FROM AUTHOR]